From bd55682f8e5f654298d87a0540a77580f8274a4d Mon Sep 17 00:00:00 2001
From: danilotat <danilotatoni@gmail.com>
Date: Thu, 12 Sep 2024 11:03:24 +0200
Subject: [PATCH] CI using official Snakemake action

---
 .github/workflows/testing.yml | 23 ++++++-----------------
 1 file changed, 6 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 2d839ec..4e5c3d5 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -11,21 +11,10 @@ jobs:
   Testing:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - name: Testing workflow
+      uses: snakemake/snakemake-github-action@v1.22.0
       with:
-        python-version: 3.8
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install dependencies
-      run: |
-        conda install -c conda-forge mamba
-    - name: Setup snakemake
-      run: |
-        mamba install -c conda-forge -c bioconda snakemake singularity sra-tools
-    - name: Run snakemake
-      run: |
-        snakemake --use-singularity --use-conda --cores 4
+        directory: .test
+        snakefile: .test/Snakefile
+        args: "--use-conda --use-singularity --show-failed-logs --cores 4 --conda-cleanup-pkgs cache"
+    
\ No newline at end of file